#--*- makefile -*--------------------------------------------------------------
#
#   Standard makefile
#
#------------------------------------------------------------------------------

# Path to project directory
UPDIR = ..
# Path to subdirectories
SUBDIR =
# Path to directory for binaries
BINPATH = ../bin

#
# Libraries and paths (which are not defined globally)
#

LIBS = -lAlign  -lBiopool2000 -ltools  

LIB_PATH = -L.

INC_PATH = -I.  -I../Biopool2000/  -I../tools/ 

#
# Objects and headers
#

SOURCES = Alignment.cc AlignmentBase.cc \
          Align.cc NWAlign.cc SWAlign.cc FSAlign.cc NWAlignNoTermGaps.cc \
          AlignmentData.cc SequenceData.cc SecSequenceData.cc \
          VGPFunction.cc VGPFunction2.cc \
          Substitution.cc SubMatrix.cc \
          ScoringScheme.cc ScoringS2S.cc ScoringP2S.cc ScoringP2P.cc \
          PssmInput.cc Profile.cc HenikoffProfile.cc PSICProfile.cc SeqDivergenceProfile.cc \
          LogAverage.cc CrossProduct.cc DotPFreq.cc DotPOdds.cc Pearson.cc JensenShannon.cc EDistance.cc AtchleyDistance.cc AtchleyCorrelation.cc Panchenko.cc Zhou.cc \
          ThreadingInput.cc Ss2Input.cc ProfInput.cc Sec.cc Threading.cc Ss2.cc Prof.cc ThreadingSs2.cc ThreadingProf.cc \
          ReverseScore.cc stringtools.cc \
          ClustalWSample.cpp NewickTreeFactory.cpp NewickTree.cpp UpgmaAlgorithm.cpp ScoringM2M.cc FastaHandler.cpp

OBJECTS = Alignment.o AlignmentBase.o \
          Align.o NWAlign.o SWAlign.o FSAlign.o NWAlignNoTermGaps.o \
          AlignmentData.o SequenceData.o SecSequenceData.o \
          VGPFunction.o VGPFunction2.o \
          Substitution.o SubMatrix.o \
          ScoringScheme.o ScoringS2S.o ScoringP2S.o ScoringP2P.o \
          PssmInput.o Profile.o HenikoffProfile.o PSICProfile.o SeqDivergenceProfile.o \
          LogAverage.o CrossProduct.o DotPFreq.o DotPOdds.o Pearson.o JensenShannon.o EDistance.o AtchleyDistance.o AtchleyCorrelation.o Panchenko.o Zhou.o \
          ThreadingInput.o Ss2Input.o ProfInput.o Sec.o Threading.o Ss2.o Prof.o ThreadingSs2.o ThreadingProf.o \
          ReverseScore.o stringtools.o \
          ClustalWSample.o NewickTreeFactory.o NewickTree.o UpgmaAlgorithm.o ScoringM2M.o FastaHandler.o

TARGETS = alitest subali alignsec aliscore blastm6test blast2fasta checkprofile bdbm5 \
#         S2S_AGP  S2S_AGP_SEC  S2S_AGP_SS2  S2S_VGP  S2S_VGP_SEC  S2S_VGP_SS2 \
          P2S_AGP_HEN  P2S_AGP_PSIC  P2S_AGP_DIV  P2S_AGP_SEC  P2S_AGP_SS2 \
          P2S_VGP_HEN  P2S_VGP_PSIC  P2S_VGP_DIV  P2S_VGP_SEC  P2S_VGP_SS2 \
          P2P_AGP  P2P_AGP_SEC  P2P_AGP_SS2  P2P_VGP  P2P_VGP_SEC  P2P_VGP_SS2 \
          MULTIALI  HEN  PSIC  DIV 

EXECS = alitest subali alignsec aliscore blastm6test blast2fasta checkprofile bdbm5 \
#       S2S_AGP  S2S_AGP_SEC  S2S_AGP_SS2  S2S_VGP  S2S_VGP_SEC  S2S_VGP_SS2 \
        P2S_AGP_HEN  P2S_AGP_PSIC  P2S_AGP_DIV  P2S_AGP_SEC  P2S_AGP_SS2 \
        P2S_VGP_HEN  P2S_VGP_PSIC  P2S_VGP_DIV  P2S_VGP_SEC  P2S_VGP_SS2 \
        P2P_AGP  P2P_AGP_SEC  P2P_AGP_SS2  P2P_VGP  P2P_VGP_SEC  P2P_VGP_SS2 \
        MULTIALI  HEN  PSIC  DIV 

LIBRARY = libAlign.a

#
# Install rule
#

compile: all

install: $(LIBRARY) $(TARGETS)
	mv $(LIBRARY) $(UPDIR)/lib
	cp $(EXECS) $(BINPATH)

#
# Call global Makefile to do the job
#

include ../tools/Makefile.global
